The Eagle's Apple
by WolfoftheMoonStorm
Summary: Juno escaped. The world was saved. But all at the same cost: Desmond Miles is dead. Juno is waiting for her chance to strike, and the human race has only once chance to fight back. And it all revolves around the Pieces of Eden and two people with dormant DNA. OC. Probably no pairings.
1. Chapter 1

**The Eagle's Apple**

_**Chapter 1**_

* * *

At first, the only thing surrounding him was darkness. Endless, endless darkness. He breathed it in, became part of it, saw nothing in its nonexistent depths. He had only one memory, or at least, he thought it was a memory. He knew of something like a consciousness, but he was not one. Bits of information floated around in the darkness that he was part of, and he simply knew it, because he was the information. But at the same time, he wasn't. Over time, he took on a shadowy form, hidden seamlessly in the darkness, but he didn't know what he was. He felt something disconnect from the eternal darkness around him, and he gained his own mind. It was weak, and vanished at times, but now he could remember his time in the darkness, instead of always knowing, but never remembering.

Then, a memory came, one he tried and failed to push away, to hide from, and now he would always remember it. He would never understand where this memory came from. It was foreign to the darkness, something for his weak mind only, and it ceased to exist when his mind did, and existed again when his mind returned.

_Burning, sorrow, betrayal, grief, acceptance, trust, hate, love, pain, darkness, light, hope, despair. An endless flow of twisted emotions, colliding with and covering one another, confused and raw. Then, the pain disappeared and everything made sense one last time. And then he forgot, and there was only the endless darkness._

The memory faded from his unwarned mind, and something told him that he hadn't wanted the memory to return in the first place. His shadowy form pulsed with foreign information, something that did not belong in the place that he was. The darkness around him rejected the foreign information, and he was unfeeling again when it disappeared.

This was his nonexistence. He did not think nor feel, but he was undisturbed by it, and simply accepted it. It had no reason or logic, and there was a mystery of no answers behind it, but it just _was_. So it was not questioned, just accepted.

He wasn't sure when it first came into the darkness, or even when he had first noticed it, but the endless darkness was no longer dark. Strands of light, dim at first, had etched themselves into the darkness. Fading and beginning in an endless pattern that repeated itself over time. The patterns slowly brightened until the light was a vivid white, tinted with gold, which lit up the endless world around him and illuminated his shadowy form that still remained unseen. It was a simple recognition at first; he couldn't actually see the light, but he could somehow tell they were familiar to… something. He wasn't sure what the something in him was that recognized the light, but it was him and not him at the same time.

And one day, he opened his nonexistent eyes.

The light was the amazing, and he felt the foreign information that he recognized as emotion creep up on him. His form prickled with awe, frozen into an ever changing position. The feelings became not-solid* and his mind told him of disbelief. The scene around him should not be real. Not in any dimension, or universe, or plane of existence. It was endlessly beautiful, something that surpassed what even an immortal being could comprehend. The light danced in ways unimaginable, calling his attention and filling him with a reminder of life. He saw all of the ages of existence pass before his eyes, storing themselves into the back of his mind. The light hummed at him, singing a tune he couldn't hear as it moved to its own sound.

It took him time to realize that the light had truly gone now, that what he was looking at wasn't there. It was just a gift the actual light had left him, to be forever caught in its grace. He was in his own mind when the darkness hadn't claimed it, and every time he left the darkness he was swallowed by the endless patterns of light.

Familiar patterns of light.

Snatches. Swirls of memory. Remembered and forgotten in the same instance. Locked away behind a gate with a missing key.

Something was coming. Getting closer as the still time passed. And the gift of the light told him of it. Hummed it into his ears. Warned him. Guided him. Reminded him.

And then the day came.

* * *

The figure breathed heavily for a moment, fear racing up and down its spine as it struggled to lock away the distracting emotion. Unwanted memories tried to edge into its mind, but the figure shook its head with an angry huff. The figure waited patiently until the unblinking eye of the camera above turned away and dashed through the shadows, throwing itself against the wall just as the next camera turned to stare unseeingly at the hall. The exposed bulbs of overhead lights flickered dimly, swaying precariously on the chains that held them to the ceiling as an outside wind entered the dim hall. The figure froze as a metal door slammed shut farther back the way the figure had come from. The figure spoke only to mutter a curse and moved quickly down the hall, desperately avoiding the cameras by hiding in the shadows under them. It wasn't safe, but it was the only choice left now.

The figure passed a multitude of identical metal doors with small glass plates labeling them overhead. Clearance numbers where handles should be acted as keys that denied the figure access again and again, but the figure ignored the red-lit numbers as it moved rapidly down the hall. The figure's breathing eased some as the cameras disappeared. Not even security was supposed to know what was farther down this hall.

A silent prayer came from the figure's lips as it expressed its thanks for the paranoia of its enemies. The figure adjusted its grip on the ball of golden metal in its hands. A soft hum came from the metal and the figure grinned in victory for a moment as a dim glow barely illuminated its hand. The figure stopped at the very end of the long hallway. An unmarked door sat in its way, the metal black instead of grey. A mixed sense of victory and foreboding swamped the figure as the fingers of its free hand slipped into a pocket and pulled out a tiny silver key.

The figure slipped the key into the tiny lock in the middle of the door and turned it to the left. A click notified the figure that the door was unlocked and the figure pulled the key out and pushed open the door. The ominous door opened in complete silence, revealing the darkness of the unlit room behind it.

The figure stepped in and immediately slid into the nearest shadow as the lights flickered on and the door behind shut with a soft thud. The room was filled with tall, round glass containers supported on elevated metal stands. Most of tops were closed with thick metal lids that had long pipes connected to the ceiling above attached to them. Others were opened, the small circular end of the pipes exposed to the open air where the metal lid should be. The closed containers were filled with a deep blue colored liquid, unfamiliar figures floating upright inside them.

The figure held perfectly still for a time, breathing light and slow to stay as quiet as possible. When it was apparent that the figure was alone, it let out a soft sigh of relief and moved through the room, scanning the plaques in front of the containers in search of something. The figure shivered slightly in the freezing room, unsurprised when puffs of white air escaped past its frozen lips. The figure's footsteps tapped quietly on the hard stone floor, the only sound in the still room.

The metal in the figure's hand slowly hummed louder, the light waking up and shining ever more brightly. The figure paused to glance at the metal for a moment, and then looked up. A sorrowful smile, filled with an endless mixture of opposite emotions, crossed the figures expression as it looked at the figure in the glass container to its right, a couple of rows down. The figure slowly approached the container and read the brass plaque in front of it, mouth moving to form the words it saw.

The metal's hum became more insistent and impatient, and the glow flickered brightly as though telling the figure to hurry. The figure shot an amused glare towards the metal in its palm, but held the golden ball of metal up. A sting of words from a strange language were formed with the figure's voice, and the ball hummed almost happily as golden tendrils of pattern-filled light surrounded the container in front of it.

A hairline crack appeared near the top of the glass.

The strange chant continued and the figure's eyes glowed the same golden color as the light emitted from the ball of metal.

The crack extended downward some and the air around the container slowly grew warmer.

The form inside the container twitched, fingers moving slightly and orbs roving beneath thin eyelids.

The air warmed and hummed along with the metal, the light began to shine blindingly. The chant changed; the words more insistent and the tone encouraging- as though asking for something.

The metal hummed. The light danced to an unheard song. The glass cracked. The ground blackened. The air burned. The golden metal came to life. A silent explosion. Blinding light. The chant ended. Golden-brown eyes opened.

And everything went dark.

* * *

She let out a silent groan and opened her eyes, their blue tinted with a golden color in the back of her iris. The container in front of her was shattered, and she gingerly sat up and moved away from a jagged shard of glass next to her. Her temples throbbed with a coming headache and she placed one hand on her head. Her gaze swept over the scene in front of her, enjoying the dissipating warmth of the air while she could.

The ground was dented in places and scorched black in others. The cryonic** chamber was broken beyond repair, and the metal platform supporting it was warped and bent into an unrecognizable position. The pipe connected to the lid seemed undamaged, half-holding the teetering metal lid that had become unclipped from the long piece of metal. The deep blue liquid was spread out in a thin puddle around the floor, rippling with the slightest movement.

Across from her, the form that was just in the glass container was on its side on the floor, eyes closed. He was breathing steadily, sleeping from the process he had just gone through. The golden ball of metal was nowhere to be seen, but her keen eyes spotted the faint golden patterns moving on his skin before they disappeared. An ironic smile crossed her expression, her eyes filled with dark amusement. _It worked._ She thought, unwillingly victorious.

She rose to her feet, aching muscles and tired bones protesting against the action. She shook her head to clear it and stretched; her spine popped and she felt a feeling of relief as the tenseness in her back vanished. She walked over to the other figure, avoiding the glass, and stood next to him, looking down with a blank expression. _Now what?_ She thought stupidly, and one palm made a quick introduction to her face. She let out an aggravated sigh and crouched down to drag the figure away from the shattered cryonic chamber and leaned him up against an empty one nearby.

Both of their clothes were soaked through and the most of the lights overhead went out with the explosion. She knew they didn't have long, but she couldn't carry him all the way out. Her gold-tinted eyes flickered around warily before she allowed the familiar rush of warmth and foreign power to flow through her. Golden patterns of light lit up dimly under her skin and she pressed the first two fingers of her right hand to his left wrist. The golden patterns sparked to life under his skin and his eyes opened, although they were glazed and unseeing.

She let out a sigh of relief and tugged him to his feet. The Apple that was now inside of him turned his head to look at her, as though the ball of golden metal was curious about what she was doing. She sighed and held up one patterned hand and the Apple made his head nod. She turned and began walking towards the door, the Apple making him follow her.

As she passed the shattered cryonic chamber, her eyes moved unbidden towards the amazingly still standing brass plaque. A certain weight settled in her stomach as her eyes moved over the words etched into its smooth surface, and she shivered slightly. Some instinct told her that _something _was coming. That something was going to happen.

Shouts and footsteps echoed far down the hallway outside the door, and she reread the words on the plaque one last time.

_Subject 17, Desmond Miles_

* * *

*** So, you know when you get ultra-frustrated or excited or something, and you get that weird feeling somewhere in your body (like around your chest or something) that feels tight or warm? That's what I mean by "not-solid." 'Cause, your emotions have no physical form (electrical pulses in brain and all that other weird biology stuff not included), but they kind of feel like they have some sort of physical form somewhere inside when they're intense like that or something, so… yeah.**

**** "Cryonic" is the correct word for the low-temperature preservation of humans or other organisms. It is often mistaken with the word "cryogenic" in literature. "Cryogenic" is the term for the study of production and behavior of materials at very low temperatures.**

**I was listening to "Byzantium" on the Assassin's Creed: Revelations soundtrack while writing about the light, so just imagine the pretty patterns of the Apple swirling endlessly around Desmond against a pitch black background (that doesn't exist 'cause it's endless darkness) while listening to it, and you get the general idea of what Desmond was looking at, and I'm kind of jealous because I think it would look beyond awesome and ridiculously beautiful and now **_**I**_** want to see it. XD**

"**She" is purposely unnamed for the beginning chapters.**


	2. Chapter 2

**The Eagle's Apple**

_**Chapter 2**_

* * *

It was a long run back through the now-darkened hallway, but she was grateful that the cameras had died with the flux of Eden energy. The shouts of the guards gave her plenty of warning to the location and movement of their enemy, and it was a simple task to lead the Apple-controlled Desmond out of the hall and through the door.

It was a less simple task to get him into the elevator and out of the Abstergo Entertainment building two floors up. She pulled the hood of Desmond's jacket over his head and forced herself to not hesitate when the elevator door opened to the main floor. She kept her pace even and ensured that she went around the back of the coffee stand, more accurately Shaun, and pretended to be curious about the ever-changing pictures on the wall. The one she was currently faking be fascinated with was a picture of Edward Kenway leaping from the Jackdaw to another brig from the main mast.

When she tilted her head down slightly to peer at Desmond's eyes under his hood, she could see the faint golden glow from the Apple as it worked, and she was certain her eyes were doing the same thing since the other Apple had to use her own to know where it was going, which meant she had to be actively using hers. She moved her eyes around quickly, making it seem as though she was just trying to look everywhere at once because she was so fascinated, in an attempt to hide the glow. She blinked more than she normally should have, knowing that just moving her eyes wouldn't hide the glow. Thankfully, most people don't watch how often a person blinks.

They had almost reached the exit and she turned to walk down the stairs when she made the mistake of looked up. Straight into the eyes of a familiar girl with black hair. _Shit,_ she cursed internally as she moved her eyes away, pretending not to pay any attention to the other girl. She prayed that the other hadn't noticed, but she couldn't fool herself for long.

She had seen the look in Rebecca's eyes. Rebecca had noticed the golden glow in her eyes. How she blinked too fast. She was grateful she had pulled Desmond too quickly down the stairs for Rebecca to notice him.

It took all her willpower not to bolt the minute they made it outside the building. She turned right and began the long walk towards the safest place nearby, the Apple-controlled Desmond following close behind.

The place she had chosen was a sturdy, one-story building with two bedrooms, a bathroom, a living room, and a kitchen, near the edge of the city. The electricity and water worked, and there was a stable internet connection that she had managed to secure from the Templars. She had made a small dinner for herself after guiding Desmond into the second bedroom in the house. The Apple had become dormant again the minute Desmond's eyes had closed and he had slipped back into his sleep.

Desmond would be like that for the next few days as he recovered from, well, coming back from the _dead_ and absorbing a _Piece of Eden _into his body.

She closed her eyes at the thought and sat back against the cream couch in the living room. Her "borrowed" laptop rested on her knees and her fingertips ran aimlessly over the keys, not really pushing any buttons. Her unfocused gaze came to rest on the bright screen, her eyes aching slightly as they adjusted to the brightness in the dark room.

She prepped herself with a huffed out sigh and closed her eyes as she opened the necessary program and waited for the screen to load. She clipped on a file attachment and left everything unnamed. The mouse hovered over the necessary button for a moment as she hesitated. Then she swallowed, and clicked send.

Across the city, a group of three people awoke to the sound of a computer alerting them of an email from an unidentified sender.

* * *

"Bill. Bill, wake up." Rebecca's voice jarred him from the middle of a confusing dream. He sat up slowly, blinking as he tried to take his surrounds. "'A'v'ca?" He muttered sleepily, shaking his head to clear it. "Rebecca?" He repeated more clearly. William took a moment to examine his surroundings.

He had apparently fallen asleep on the couch. Again. All the lights in the room were off, so he could only see what was illuminated by the blue-tinted light of the computer. The window revealed it was close to 2:00 AM. Shaun, sitting in the desk chair, was obstructing some of the light from the computer, and Rebecca was standing over him, one hand extended as she helped him stand.

William yawned, "What happened?" Nothing seemed out of place, or out of the ordinary. They hadn't been attacked, and an alarm would be going off on the computer if one of the other hideouts had been attacked. "Absolutely nothing. Yet." Shaun answered and William snapped awake at his tense tone. He remained silent as Rebecca walked towards the computer, patiently waiting for an explanation.

"We received an email from someone, but we don't know who. And it's very…" Rebecca trailed off.

"Trap worthy." Shaun supplied and Rebecca nodded, shrugging slightly.

"It's worrying, at the least, and then there's these letters." Rebecca added and William moved forward to read the email.

* * *

Sender: -

Subject: (No Subject)

I know you don't trust th_i_s email. That's good. It'd b_e_ stupid if you did. But you still need to do what I say. You can trac_e_ the computer I sent this me_s_sage on. It's on a secure channe_l_; the Templars can_'_t get to it. But only for three days. Co_m_e to this address. I won't be here. _D_estroy the computer you find here.

There's a POE absorbed int_o_ DNA. Figure out how to co_n_trol it. Ask the Roman Athena when she pops up for answers. Roman Hera isn't very h_a_ppy about this, but she can't do much now. Sage is _d_angerous. The S17 project need_s_ to be stopped.

Read the _letters_.

Find the hidden truth.

You ha_v_e three days to decide. Choose wisely.

* * *

"_Find the hidden truth." _William read aloud. Shaun nodded and Rebecca reread the message.

"What do we have so far?" William asked.

"The 'hidden truth' is in the message they sent us. The clue for that is the way it's written. The first paragraph is instructions. The second paragraph is information. The last three sentences are about the email. 'Roman Athena' refers to Minerva, and 'Roman Hera' refers to Juno. The 'Sage' bit is puzzling, but if we assume that whoever this is knows what we know about the Observatory, then the answer is that the Sage isn't on our side. The word 'letters' is italicized, like specific letters in the message. From what we've been able to tell about this secure channel, if someone hacked the email and tried to look at it, all of this would pop up in one long paragraph in a different font, and the letters that are italicized wouldn't appear like they were. 'S17' is Subject 17. But there's one thing that doesn't make sense." Rebecca listed off as Shaun tapped away on the keyboard, running tests on the email.

"From what I've been able to tell so far, whoever sent this isn't lying, and isn't trying to trick or trap us. This channel is completely cut off from Abstergo or any Templar related _thing_ on the planet. My guess would be that even the other computer wasn't made by Abstergo." Shaun spoke up and William felt a flicker of surprise. That wasn't an easy feat to pull off.

"The thing that doesn't make sense is this sentence." Shaun pointed at the screen, _"There's a POE absorbed into DNA._ 'POE' definitely stands for Piece of Eden, but that's just impossible."

"We're dealing with the First Civilization; the impossible seems to be pretty possible." William replied bluntly. "Rebecca, write those slanted letters down in order on a sheet of paper, Shaun, try to figure out exactly how secure the channel is without cracking it. This person seems fairly certain it'll be fine for three days, but I want to know exactly how much time we have. See if you can get a clue about the sender to. Whoever it is seems to know a lot."

They responded quickly to his orders as he stood in the darkened room, watching Shaun work and searching his mind for answers. He turned the email over in his head. The email wouldn't make much sense to a normal person, and a Templar might have been able to crack it, but without the correct appearance of the email, they would still miss a lot of the true message. Whoever sent this email sure went through a lot of trouble to be cryptic.

"Here, I got it, but it doesn't make any sense." Rebecca said as she held out a sheet of paper and switched on the nearest lamp.

William set the paper down on the desk and Shaun paused to read it.

**ieesl'mDonadsv**

William tried saying the letters like a word in his head, but it came out as meaningless gibberish. He gritted his teeth. This was either a trick, or it was the most important thing in the email. "What are we supposed to do with this?" Rebecca muttered, her brows furrowed in confusion.

Silence filled the room as the three Assassins wracked their brains.

"It's a scrambled word." Shaun breathed, his eyes wide in realization. William turned to look at him. "It's a what?"

"A scrambled word. It's one or more words with the letters mixed up." Shaun said in a louder voice. He turned to the computer in front of him and clicked open a couple different applications. He tugged the paper closer to him and typed the letters into a small box on the screen. The mouse clicked one more time and a list of words popped up below the box. Shaun scrolled down in slowly, and all three of them skimmed through the list, looking for something that rang a bell or seemed important.

"Try a different site, Rebecca. They get different results sometimes." Shaun said and Rebecca pulled her phone out of her pocket. William paid little attention to the sounds of the keyboard clicks next to him, and silence filled the room a moment later. A few minutes passed as they refreshed the results and tried different un-scramblers.

"Holy crap." Rebecca's voice broke the silence and she stared at her phone as if she had never seen it before. She was pale as a sheet of paper, and the mixed lighting from the lamp and computer made her look inches from death.

"What did you find?" William asked, his tone sharp.

Rebecca turned the phone around slowly, her eyes wide with disbelief. Shaun and William looked down at the phone, reading the seventh word down that her thumb was pointing to.

**Desmond's alive**

A tense silence crossed the room as they stared at the tiny words on the screen. Shaun slipped back into his chair with a thud and William sat down heavily on the couch. "_That's_ impossible. We know he's dead. We saw the footage of the Templars finding his… body. Just… no…" William covered his face with one hand, and exhausted sigh escaping him and he suddenly felt ages older than he really was. "That can't be the right combination. It can't be 'Desmond's alive'."

The email alert went off and the opened email on the screen suddenly expanded. _'View Attachment'_ appeared below the message. Shaun stared, "Transferred spoken phrase voice activated email reveal? What kind of program did they _use_?"

"Open it." William ordered, and Rebecca shot a worried glance toward him, but didn't speak up.

Shaun clicked open the attachment and an image appeared on screen.

"Holy crap." Shaun agreed, and the email holding a video of a sleeping Desmond deleted itself.

* * *

**I had fun with this chapter for some weird reason. Anyways, I hope you enjoyed. Just in case, I'm warning you now that this is a slow story, and thus long.**


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